I notice that some kegs have fairly long diptubes (about 3 inches) at the "In" connection, while others are much shorter. The long ones mean that you can't fill them as full, since the volume should be below the level of the diptube.

Is there any particular reason why these tubes should be of any particular length? I was wondering if I could cut them all to a shorter length to allow for more beer to be aded to the keg. As it is, I cannot get all of the five gallons from the fermenter (minus the trub) into the keg. There's always a pint or two left over.

I have also filled all my kegs above the bottom of the dip tube. I have never had a problem. If you ensure you don't let the keg pressure get above the gas pressure, while liquid is above the bottom of the tube, you won't have to worry about beer flowing into your regulator.

Think about the people that attach a carb stone to a long dip tube. They don't open the keg up and take it out when the keg is ready they just serve with the stone in the beer, unless you use the carbing lid.

I say leave it and put a check valve on your gas line so you don't worry about beer flowing back into your regulator if something goes wrong.

Check valve definitely. If not, it really depends on your practices. If you force carb rather than set and forget you will probably have a higher chance of getting beer into the gas lines when you hook them up.

I use sanke kegs so this is less relevant to me but you should definitely have check valves. Even just the beer warming up a bit can cause the pressure to increase above the level of the regulator, causing back pressure to the co2 line. Obviously if the co2 tube is in the beer its worse, but I wouldn't want anything going into the co2 system (manifolds, reg's, whatever) once its been in the keg.